Jacques Dainat
in GFF3 ```URL escaping rules are used for tags or values containing the following characters: ",=;". Spaces are allowed in this field, but tabs must be replaced with the %09...
Hi, Thank you for using AGAT. Yes it is because the "cDNA_match" are level1 feature (l1 feature does expect child features linked to it, thus need to be identifieable with...
The first issue make me think that there are error in the strand column of your gff file. Could you show a sample of your file? The second error is...
When developing this script I was using exonerate output From MAKER. Either you do not use the correct command, or MAKER was doing extra manipulation before outputing the exonerate gff....
Yes sure: ``` unitig_6|quiver protein2genome protein_match 162828 163298 359 - . ID=unitig_6|quiver:hit:874:3.10.0.1;Name=B4G8R5.1 unitig_6|quiver protein2genome match_part 162828 163298 359 - . ID=unitig_6|quiver:hsp:1613:3.10.0.1;Parent=unitig_6|quiver:hit:874:3.10.0.1;Target=B4G8R5.1 130 287;Length=311;Gap=M35 I2 M51 I2 M31 D3 M37 unitig_6|quiver...
Instead of using the `Gap` attribute to compute the identity on the fly I can directly take the `identity` or the `similarity` score. In the same way we can use...
I need a sample of your annotatoin gff file on which you want to lift the protein information on
Actually the use of CIGAR is preferable than vulgar. We need `--showcigar yes` rather than `showvulgar`. The GAP attribute in GFF3 is based on CIGAR. That might simplify a lot...
I have not seen any easy way to fix that. I'm not able to reproduce the MAKER polishing allowing to have a neat information to judge the overlapping quality to...